Acanthopagrus latus is an essential aquaculture species on the south coast of China.However,there is a lack of systematic breeding of A.latus,which considerably limits the sustainable development of A.latus.As a resul...Acanthopagrus latus is an essential aquaculture species on the south coast of China.However,there is a lack of systematic breeding of A.latus,which considerably limits the sustainable development of A.latus.As a result,genetic improvements are urgently needed to breed new strains of A.latus with rapid growth and strong resistance to disease.During selective breeding,it is necessary to estimate the genetic parameters of the target trait,which in turn depends on an accurate disentangled pedigree for the selective population.Therefore,it is necessary to establish the parentage assignment technique for A.latus.In this study,95 individuals selected from their parents and their 14 families were used as experimental material.SNPs were developed by genome resequencing,and highly polymorphic SNPs were screened on the basis of optimized filtering parameters.A total of 14392738 SNPs were discovered and 205 SNPs were selected for parentage assignment using the CERVUS software.In the model where the gender of the parents is known,the assignment success rate is 98.61%for the male parent,97.22%for the female parent,and 95.83%for the parent pair.In the model where the gender of the parents is unknown,the assignment success rate is 100%for a single parent and 90.28%for the parent pair.The results of this study were expected to serve as a reference for the breeding of new varieties of A.latus.展开更多
The large yellow croaker Larimichthys crocea is one of the most important fish species in China. To estimate the re- productive success of breeders, three independent full-factorial crosses were created and the fins o...The large yellow croaker Larimichthys crocea is one of the most important fish species in China. To estimate the re- productive success of breeders, three independent full-factorial crosses were created and the fins of breeders and progenies were sampled for microsatellite analysis. Out of 959 offspring from three sets, 99.6% were assigned to their parents using 6-7 mi- crosatellite markers. In all crosses, some parent pairs produced a large number of offspring and some parent pairs did not produce any offspring. The contributions of male or female parents were unequal, ranging from 1.0-89.3% across the three sets. The loss of putative Ne was 69.6% in set 1, 31.2% in set 2 and 57.6% in set 3. These results suggest that the unequal contribution of parents is universal in artificial breeding ofL. crocea, especially in a small population, and this should be taken into account in hatcheries or when releasing animals for resource enhancement展开更多
Scapharca broughtonii is a commercially important and over-exploited species.In order to investigate its genetic diversity and population structure,43 novel polymorphic microsatellites were isolated and characterized....Scapharca broughtonii is a commercially important and over-exploited species.In order to investigate its genetic diversity and population structure,43 novel polymorphic microsatellites were isolated and characterized.The number of alleles per locus ranged from 3 to 22 with an average of 6.93,and the observed and expected heterozygosities varied between 0.233 and 1.000,and 0.250 and 0.953,with an average of 0.614 and 0.707,respectively.Three highly informative multiplex PCRs were developed from nine of those microsatellites for S.broughtonii.We evaluated and validated these multiplex PCRs in 8 full-sib families.The average polymorphism information content(PIC) was 0.539.The frequency of null alleles was estimated as 3.13% of all the alleles segregation based on a within-family analysis of Mendelian segregation patterns.Parentage analysis of real offspring demonstrated that 100% of all offspring were unambiguously allocated to a pair of parents based on 3 multiplex sets.Those 43 microsatellite loci with high variability will be helpful for the analysis of population genetics and conservation of wild stock of S.broughtonii.The 3 sets of multiplex PCRs could be an important tool of pedigree reconstruction,population genetic analysis and brood stock management.展开更多
Iwagaki oyster,Crassostrea nippona,widely distributes along the seashore of Eastern Asia,and has been considered to be a potential breeding species due to its delicious taste and high commercial value.In order to stud...Iwagaki oyster,Crassostrea nippona,widely distributes along the seashore of Eastern Asia,and has been considered to be a potential breeding species due to its delicious taste and high commercial value.In order to study its genetic background and population structure,we developed 46 novel polymorphic microsatellite markers using next-generation sequencing technique and characterized them in 30 individuals.The number of alleles ranged from 3 to 22,while the observed and expected heterozygosities varied from 0.133 to 1.000 and 0.455 to 0.949,respectively.Fifteen microsatellite markers were selected and grouped into five highly informative multiplex PCRs for C.nippona.We evaluated and validated these multiplex PCRs in a cultured population including 173 candidate parents and 486 offspring.In actual parentage analysis,80%of the offspring were correctly assigned to their parental pairs using three multiplex PCRs.Furthermore,the success rate of parentage assignment reached 96%when the other two multiplex PCRs were added.These 46 microsatellite loci with high variability and the five multiplex PCRs described here provide a powerful tool for pedigree reconstruction,resource conservation and selective breeding program of C.nippona.展开更多
Heritability estimates may be severely biased when a large common environmental effect on a family arises from a longlasting separate rearing at early stages(SRES)in traditional selective breeding programs,especially ...Heritability estimates may be severely biased when a large common environmental effect on a family arises from a longlasting separate rearing at early stages(SRES)in traditional selective breeding programs,especially when bred populations have weak genetic ties.Communal rearing at early stages(CRES)may reduce common environmental effect since all families are reared in the same environment immediately after hatching.Here,we compared the effects of CRES and SRES strategies on genetic parameter estimation for harvest body weight in a selective breeding population of Litopenaeus vannamei with a small number of half-sib families.Genetic parameters of each strategy were estimated by using animal models excluding and including the common environmental effect(Model 1 and Model 2,respectively).Heritability estimates for body weight were 0.21±0.06(P<0.05)and 0.69±0.09(P<0.05)for CRES and SRES,respectively,in Model 1,and 0.21±0.06(P<0.05)and 0.52±0.27(P>0.05)in Model 2.The ratio of common environmental variance to phenotypic variance was 0.002±0.000 and 0.071±0.112 for CRES and SRES,respectively.Neither strategy precisely partitioned the common environmental variance according to likelihood ratio test.Lower heritability for body weight in CRES than in SRES implied that a large common environmental variance was confounded with additive genetic variance and was not effectively partitioned in SRES.Moreover,genetic correlation of body weight between the two strategies was 0.75±0.15,indicating that family rankings truly changed.The CRES should be followed in the selective breeding program of shrimp,especially in a population with a shallow pedigree and weak genetic ties between families.展开更多
基金Fujian Province science and technology plan project under contract No.2023N0011。
文摘Acanthopagrus latus is an essential aquaculture species on the south coast of China.However,there is a lack of systematic breeding of A.latus,which considerably limits the sustainable development of A.latus.As a result,genetic improvements are urgently needed to breed new strains of A.latus with rapid growth and strong resistance to disease.During selective breeding,it is necessary to estimate the genetic parameters of the target trait,which in turn depends on an accurate disentangled pedigree for the selective population.Therefore,it is necessary to establish the parentage assignment technique for A.latus.In this study,95 individuals selected from their parents and their 14 families were used as experimental material.SNPs were developed by genome resequencing,and highly polymorphic SNPs were screened on the basis of optimized filtering parameters.A total of 14392738 SNPs were discovered and 205 SNPs were selected for parentage assignment using the CERVUS software.In the model where the gender of the parents is known,the assignment success rate is 98.61%for the male parent,97.22%for the female parent,and 95.83%for the parent pair.In the model where the gender of the parents is unknown,the assignment success rate is 100%for a single parent and 90.28%for the parent pair.The results of this study were expected to serve as a reference for the breeding of new varieties of A.latus.
基金Aeknowleflgements Thanks to Chen Qing-kai for rearing fish families. This study was supported by Special Fund for Agro-scientific Research in the Public Interest （200903029-4）, the National Natural Science Foundation of China （30771663）, Key Project of Fujian Provincial Department of Science ＆ Technology （2010N0021）, the Foundation for Innovation Research Team of Jimei University, China（2010A002） and the Open Foundation from Ocean Fishery Science and Technology in the Most Important Subjects of Zhejiang （20100203）.
文摘The large yellow croaker Larimichthys crocea is one of the most important fish species in China. To estimate the re- productive success of breeders, three independent full-factorial crosses were created and the fins of breeders and progenies were sampled for microsatellite analysis. Out of 959 offspring from three sets, 99.6% were assigned to their parents using 6-7 mi- crosatellite markers. In all crosses, some parent pairs produced a large number of offspring and some parent pairs did not produce any offspring. The contributions of male or female parents were unequal, ranging from 1.0-89.3% across the three sets. The loss of putative Ne was 69.6% in set 1, 31.2% in set 2 and 57.6% in set 3. These results suggest that the unequal contribution of parents is universal in artificial breeding ofL. crocea, especially in a small population, and this should be taken into account in hatcheries or when releasing animals for resource enhancement
基金supported by National Marine Public Welfare Research Program(201205023)National Natural Science Foundation of China(41276138)Doctoral Program of Ministry of Education of China(2013 0132110009)
文摘Scapharca broughtonii is a commercially important and over-exploited species.In order to investigate its genetic diversity and population structure,43 novel polymorphic microsatellites were isolated and characterized.The number of alleles per locus ranged from 3 to 22 with an average of 6.93,and the observed and expected heterozygosities varied between 0.233 and 1.000,and 0.250 and 0.953,with an average of 0.614 and 0.707,respectively.Three highly informative multiplex PCRs were developed from nine of those microsatellites for S.broughtonii.We evaluated and validated these multiplex PCRs in 8 full-sib families.The average polymorphism information content(PIC) was 0.539.The frequency of null alleles was estimated as 3.13% of all the alleles segregation based on a within-family analysis of Mendelian segregation patterns.Parentage analysis of real offspring demonstrated that 100% of all offspring were unambiguously allocated to a pair of parents based on 3 multiplex sets.Those 43 microsatellite loci with high variability will be helpful for the analysis of population genetics and conservation of wild stock of S.broughtonii.The 3 sets of multiplex PCRs could be an important tool of pedigree reconstruction,population genetic analysis and brood stock management.
基金supported by the National Natural Science Foundation of China (No. 31772843)the Natural Sci- ence Foundation of Guangxi Province (No. AA17204080-4)the Fundamental Research Funds for the Central Uni- versities (No. 201762014)
文摘Iwagaki oyster,Crassostrea nippona,widely distributes along the seashore of Eastern Asia,and has been considered to be a potential breeding species due to its delicious taste and high commercial value.In order to study its genetic background and population structure,we developed 46 novel polymorphic microsatellite markers using next-generation sequencing technique and characterized them in 30 individuals.The number of alleles ranged from 3 to 22,while the observed and expected heterozygosities varied from 0.133 to 1.000 and 0.455 to 0.949,respectively.Fifteen microsatellite markers were selected and grouped into five highly informative multiplex PCRs for C.nippona.We evaluated and validated these multiplex PCRs in a cultured population including 173 candidate parents and 486 offspring.In actual parentage analysis,80%of the offspring were correctly assigned to their parental pairs using three multiplex PCRs.Furthermore,the success rate of parentage assignment reached 96%when the other two multiplex PCRs were added.These 46 microsatellite loci with high variability and the five multiplex PCRs described here provide a powerful tool for pedigree reconstruction,resource conservation and selective breeding program of C.nippona.
基金the National Key R&D Program of China(No.2018YFD0901301),the Shandong Province’s Agricultural Seed Improvement Project(No.2017LZN011)the Central Public-interest Scientific Institution Basal Research Fund,CAFS(No.20603022020003)+3 种基金the China Agriculture Research System(CARS-48)the Projects of International Exchange and Cooperation in Agriculture of Ministry of Agriculture and Rural Affairs of China–Science,Technology and Innovation Cooperation Cooperation in Aquaculture with Tropical Countriesthe Introduction of International Advanced Agricultural Science and Technology Plan of China(No.2016-X39)the Major Applied Technology Innovation Project of Agriculture in Shandong Province(No.SD2019YY001).
文摘Heritability estimates may be severely biased when a large common environmental effect on a family arises from a longlasting separate rearing at early stages(SRES)in traditional selective breeding programs,especially when bred populations have weak genetic ties.Communal rearing at early stages(CRES)may reduce common environmental effect since all families are reared in the same environment immediately after hatching.Here,we compared the effects of CRES and SRES strategies on genetic parameter estimation for harvest body weight in a selective breeding population of Litopenaeus vannamei with a small number of half-sib families.Genetic parameters of each strategy were estimated by using animal models excluding and including the common environmental effect(Model 1 and Model 2,respectively).Heritability estimates for body weight were 0.21±0.06(P<0.05)and 0.69±0.09(P<0.05)for CRES and SRES,respectively,in Model 1,and 0.21±0.06(P<0.05)and 0.52±0.27(P>0.05)in Model 2.The ratio of common environmental variance to phenotypic variance was 0.002±0.000 and 0.071±0.112 for CRES and SRES,respectively.Neither strategy precisely partitioned the common environmental variance according to likelihood ratio test.Lower heritability for body weight in CRES than in SRES implied that a large common environmental variance was confounded with additive genetic variance and was not effectively partitioned in SRES.Moreover,genetic correlation of body weight between the two strategies was 0.75±0.15,indicating that family rankings truly changed.The CRES should be followed in the selective breeding program of shrimp,especially in a population with a shallow pedigree and weak genetic ties between families.
